The nightmare in the happiness
by sbfan365
Summary: Sequel to What We Could Have. Takes place 2 years after it left off. There will be some angst but some fluff too.I can't summarize without ggiving away everything that will happen so please Read and Review
1. Chapter 1

**AN: Well my muse finally decided to give me a plot so here is the sequel to What We Could Have. I hope you enjoy more fluff with a touch of angst. It takes place 2 years after What we Could Have ended if you haven't read the first story I suggest you do. Please review**

**Enjoy!**

Brennan sat at her desk in her office and looked up from her work and smiled at nothing in particular.

Many things had changed about her office and they represented the changes that had occurred in her life over the last two years. There was the picture of her and Booth from their wedding that sat next to her computer. Along her shelves were other pictures of her family. There were coloring books and toys on the coffee table which reminded her of Ali and even Savannah who happened to be coloring at the moment, because Angela who was 5 months pregnant with twins had a doctor's appointment. Thinking about babies led her eye to the pack-and-play in the middle of her office. She smiled at the thought of the latest addition to her family…Matthew Hank Booth. Matt had been a complete surprise, but a welcome one. He was a spitting image of his mother. Brennan's thoughts were interrupted by loud talking which Brennan immediately recognized as the high pitched voice of Ali. Seconds later Ali appeared in her office followed by Booth who carried 4 month old Matt in his car seat followed by 11 year old Parker who had the day off from school.

"Booth what are you doing here?" Brennan gave Booth a kiss and took the car seat from him and picked up Matt.

"Well you see Ali wanted to see you, Matt missed you, and Parker needed help with his science project." Booth joked. Brennan pretended to be upset and sat down in her chair.

"Uncle Booth, look what I colored." Savannah chimed in pronouncing Booth like Boof.

"Very nice Savannah." Booth sat down next to Savannah and looked over the 3 year old's coloring.

"Mommy can I see your work?" Ali was skipping around the room.

"Sure honey why don't you go on out to the platform and see if Angela is there." Brennan handed Ali her security card and Ali skipped out of her office singing. Savannah who heard the mention of her mom ran after Ali. Booth sent Parker after the girls to make sure they didn't get into trouble.

Booth took the moment alone to properly say hello to his wife. He took Brennan into his arms and gave her a light tender kiss. Brennan pulled back and smiled at him. "You know Matt is still here." Brennan motioned to the car seat where Matt. who had recently discovered he had hands, had shoved his fist into his mouth and was unaware of his parents gaze. Eventually he took his fist out of his mouth and squealed with delight at his parents. Brennan picked him up and headed to the platform with Booth following them.

On the platform was Angela who was trying to listen to 3 different stories from Ali, Savannah, and Parker. Luckily their attention was drawn to Booth and Brennan as they approached the platform. Ali ran over to them and Booth picked her up.

"Hey Ange, how was the doctor?" Brennan asked excitedly.

"It was good; he told us we were having a girl and a boy." Angela put a hand on her quickly expanding stomach.

"Really that's great!" Brennan did her best to give her friend a hug. Booth smiled and congratulated her.

Soon they were joined by Hodgins who was beaming. When Savannah caught sight of him she ran over to him shouting "Daddy!" Hodgins scooped her up and gave her a hug. Savannah was a perfect combination of Angela and Hodgins; she had dark almost black hair that was in perfect ringlets, warm caring brilliant blue eyes and her mother's nose. Seeing father and daughter together brought out these resemblances.

Hodgins walked over to the group on the platform with Savannah and stood by his now wife, Angela. "So I guess you guys heard the news." Hodgins beamed

"Yes, congratulations." Booth and Brennan smiled

"Uncle Jack, do you really eat bugs?" Ali interrupted. Last time she had come to the lab Hodgins had been using the blender on some maggots when Ali wandered over and asked if what he was doing, Hodgins jokingly told her he was going to eat them. Ever since, Ali had been adamant to know the truth. The adults and Parker laughed while Ali and Savannah waited for an answer.

"No, I don't eat bugs and I never will." Hodgins reassured the girls.

"Just look at my little nephew, he is getting so big!" Angela looked at Matt and smiled. Brennan handed Matt to Angela.

Eventually Cam came on to the platform to see why her team wasn't working. When she saw the kids she immediately melted. Savannah and Ali climbed down from their fathers arms and ran to give Cam a hug. "Hello Savannah and Ali what a surprise!" Cam patted the girls on the head. "Matt and Parker are here too." Ali added before she and Savannah ran back to their parents. Cam followed them.

"I hate to break up this little family reunion, but we have another case." Cam said quietly before handing the file to Booth.

"Oh I see, well then can we leave the kids here with you?" Booth asked Cam

"Of course." Cam smiled down at Ali who looked at her questioningly.

"Ok then lets go Bones." Booth turned to his partner. After saying good bye to each of their kids Booth and Brennan headed to the crime scene.

__________________________________B3B_________________________________

When Booth and Brennan got to the crime scene they got straight to work. The body had been found in the woods of a park by a young couple who were going for a jog. Upon seeing to body they called 911.

Booth went to question the couple while Brennan went to body. "The victim is female, young approximately 5 years old. Brutally beaten." Brennan looked to Booth with sadness in her eyes. "I need everything sent to the lab." Booth nodded and directed the FBI agents in gathering evidence. After another 30 minutes Booth and Brennan were ready to go back to the lab and headed to the SUV.

"Booth, this victim and the manner of death matches the last 4 cases we have had." Brennan said as Booth pulled into traffic.

"I know Bones, but we can't jump to conclusions. You told me that." Booth tried to comfort Brennan, but found it hard.

"All the victims have been young girls who were beaten and raped. All the injuries are the same on each of the victims." Brennan ignored Booth's comment. "We have to find who ever is doing this." Brennan was trying to fight tears. Cases where the victim was young were always hard, but now that she had kids of her own she found them even harder.

"I know Bones; I hate these cases just as much as you do. I hate who ever is going around killing innocent little girls." Booth was beginning to get angry. "You need to distance your self from the cases." Booth took Brennan's hand.

After a minute Brennan spoke. "You're right."

The rest of the ride was spent in silence. By the time they reached the Jeffersonian the body had already arrived. Booth and Brennan walked into the lab hand in hand using each other for support.

After the body had arrived Cam called Max who was teaching the after school program that day and asked him to take the kids while the team examined the body.

Angela was working on a facial reconstruction, Hodgins was working with the particulates, and Cam was working with what little tissue was left on the body when Booth and Brenan joined them on the platform.

"Ok what do we have so far?" Brennan asked as she put on a pair of gloves

"Nothing yet, Daisy is cleaning the bones now." Cam answered

"Ok, then I will be in my office. Please have Miss Wicks notify me when the bones are ready." The rest of the team exchanged glances as Brennan walked off the platform.

They could tell that this case was getting to her. Booth was going to go talk to her, but Angela stopped him told him she would go talk to her.

Angela made her way to Brennan's office. When entered her office she found Brennan sitting at her desk with her eyes closed. When she heard Angela come in she opened her eyes.

"Sweetie is everything ok?" Angela sat down on the couch

"I'm fine Ange; it's just really hard to work these cases." Brennan tried to keep her emotions in check.

"I know Bren, believe me I know." Angele went over to her friend

"When I look at those bones I can tell just how much each of those little girls suffered. I can't imagine how scared they must have been. How upset their parents must be to lose such a…a young innocent life." A single tear fell down Brennan's face. Angela didn't say anything for a moment. "Sweetie why don't you go home with Booth and spend some time with Ali, Matt, and Parker." Angela finally spoke.

"That sounds good." Brennan stood up and gave her friend a hug.

Brennan went back onto the platform and told Booth what she wanted to do he agreed and then they went to go pick up the kids.

_________________________________B3B_____________________________

The Booth family decided to go to the park and play. Parker and Booth tried to teach Ali how to play soccer. Brennan sat on a bench with Matt and watched. After spending 2 hours at the park the kids were hungry and tired out. The decided to go to the diner for an early dinner afterwards they dropped Parker off at Rebecca's and then headed to their own home.

They spent the rest of the day playing with the kids at home. Around 7 Booth took Ali upstairs for a bath while Brennan fed Matt. After her bath Booth dressed Ali in her favorite pink nightgown and began reading her a story. Brennan brought in Matt to listen to the story.

After reading 3 stories it was time to say goodnight

"Goodnight Ali I love you." Brennan gave her a kiss before she went to put Matt to bed.

"Night mommy, night Matt love you." Brennan lowered Matt so Ali could give him a kiss.

Brennan then went across the hall and rocked Matt in his rocking chair.

"Ok princess lights out." Booth pulled the sheets over Ali

"Goodnight daddy I love you."

"Love you too Ali cat." Booth turned off the light and closed the door to her bed room.

Booth walked across the hall to Matt's room where he stood in the doorway watching Brennan. She was still in the rocking chair holding Matt who was sucking his thumb in his sleep.

"Hey." Booth said from the doorway

"Oh, hey I was just thinking." Brennan whispered

"Yeah, what about?" Booth entered the room now.

"Nothing really, just how I wish I could have more days like today." Brennan stood up and carried Matt to his crib and laid him in it. She then grabbed the light blue blanket from the side of the crib and placed on Matt.

Booth noticed her hesitation to leave the crib and joined her. "He looks so innocent when he sleeps." Booth spoke Brenna's thought

"Yeah, I wish we could keep him like that forever." Brennan ran a finger over Matt's cheek.

"Nothing is going to happen to him. I won't allow it. The same goes for you and Ali." Booth stated Brennan's other thought.

Brennan sighed and turned towards Booth who was behind her, they looked into each others eyes for a log time before Brennan melted into his arms.

"I know Bones, these cases hurt in the worst way." Booth spoke into her hair. They stayed in that position until Booth pulled away and silently guided Brennan to their room so they could go to bed. Booth and Brennan slept peacefully not knowing that the next few months would become their worst nightmare.

AN: Well this chapter is just to set everything up for the rest of the story. REVIEW REVIEW REVIEW!!!!!!!!!!


	2. Chapter 2

**AN: Ok so here's chapter 2… Things won't be so fluffy anymore in this chapter. This is the start of their "nightmare"….well the first one. Enjoy! **

________________________________________________________________________At 6:30 Booth and Brennan were woken up by their alarm clock.

"No." Booth grumbled as he tightened his arms around Brennan, who was still asleep.

"Come on baby time to rise and shine." Booth kissed Brennan's chin.

"Five more minutes Booth." Brennan buried her head into Booth's shoulder

"No, we need to get up now" Booth kissed her hair. Brennan was going to protest again, but Matt began to cry. Brennan untangled herself from Booth and went to take care of Matt before his crying could wake up Ali. Booth went into the bathroom to take a shower.

When Booth got out of the shower he took Matt downstairs to make breakfast while Brennan took a shower and got ready. After Brennan was ready she went and woke up Ali.

She dressed Ali in a pink dress which Ali insisted needed polka-dotted tights with it. She French braided her hair and then chased her downstairs where Booth and Matt were sitting at the table waiting for Brennan and Ali to join them for breakfast.

At 8 Mary, the nanny, arrived to watch Matt. Booth and Brennan left with Ali who had preschool until 2 that day. They dropped Ali off on their way to work. "Bye princess have a good day." Booth said as Brennan helped Ali out her car seat. "Bye daddy, love you." Ali jumped out of the car and Brennan walked her into school.

___________________________________B3B________________________________

When Booth and Brennan arrived at the lab the most recent body was laid out on one of the examination tables. Angela had identified the girl as 5 year old Hannah Richards. She had gone missing 5 months ago. Her picture was placed on the board with the names and photos of the other 4 girls; Michelle Gomez, Danielle Simpson, Kayla George, and Olivia Santiago, all of the girls were between the ages of 5 and 7 years old.

Cam informed Booth that Hannah's parents had arrived from Newport News and were sitting in Brennan's office. Booth went off to talk with them while Brennan worked on the body.

"Hello, Mr. and Mrs. Richards I'm Special Agent Seeley Booth." Booth flashed his badge and sat in a chair across from the couch.

"So, you found Hannah." Mr. Richards asked.

"Yes, we had an expert do a facial reconstruction and it matched Hannah's picture." Booth showed them the reconstruction.

"That's our Hannah." Mrs. Richards started to cry.

"I have to ask, was there anyone who would want to hurt Hannah?" Booth asked.

"No, everyone loved her. She had so many friends at school." Mrs. Richards answered through her tears.

"I'm sorry, but what is the point in these questions? As you can see we are very upset about this." Mr. Richards was getting angry.

"I understand this is hard, but it's just standard procedure." Booth tried to be empathetic

"Do you have kids agent Booth?" Mr. Richards still wouldn't calm down.

"Yes, I have 3 actually." Booth's eyes flicked to the pictures on Brennan's book shelves.

"Well then you know how we must be feeling right now. Please excuse us, we will call you if have any new information" Mr. Richards stood up and his wife followed apologizing for her husband.

Booth stayed sitting in Brennan's office for a minute. Eventually he made his way to the bookshelf and picked up one of the pictures there. It was one of his favorites; Ali and Parker were under the Christmas tree, Parker was holding Matt who was more interested in his hands than the picture. Ali leaned over and kissed Matt's head. Brennan had been the one to notice the scene and take the picture.

After a few more moments Booth became aware of another presence in the office and turned around to see Brennan standing there looking at the picture too. "That's one of my favorites." Brennan smiled. "Mine too, now let's get back to work." Booth guided Brennan back to platform.

"Booth, I found cause of death. She was strangled." Cam informed Booth. "There was also evidence of rape and torture."

Booth paused for moment before he spoke. "Ok, does it fit the pattern of the other murders?"

"Unfortunately, yes." Cam looked at each member of the team. She couldn't imagine how hard it must be for them since they kids of their own.

"Ok, well then let's catch this bastard, do we have any leads?" Booth tried to get everyone motivated.

"Well I found mulch that isn't consistent with where the body was found." Hodgins piped up

"Ok, where CAN we find this mulch?" Booth was getting a little agitated

"Her school and the park across from her school both use it." Hodgins answered.

"Well then let's go see if anyone at the park remembers seeing her the day she disappeared." Booth turned towards Brennan. Brennan nodded and they both headed off the platform to the parking garage.

___________________________________B3B________________________________

"This is a much nicer park than the one we go to." Brennan noted as she and Booth wandered through the park.

"Yeah you're right. Now let's see if anyone here is a regular." Booth headed over to a bench where a group of mother's was sitting. "Hello ladies, Special Agent Seeley Booth, this is my partner Dr. Temperance Brennan, do any of you remember seeing this girl here a few months ago." The women took the picture of Hannah that Booth offered and passed it around. After everyone saw it one woman spoke up.

"I remember her, Hannah was her name. She would come here with her nanny, she and my daughter played together. She was a sweet little thing, what happened to her?"

"She was brutally raped and murdered." Brennan spoke up. Booth gave her a "let me handle this" look.

"Oh my, well the last time I saw her was around March. She was going to go down the slide and then we never saw her again." The woman offered more information.

"And what is her nanny's name?" Booth asked with his pen and notepad ready.

"Isabel Davis. She was so upset when she lost Hannah." The woman shook her head.

"Thank you Ms…I didn't quite catch your name." Booth paused.

"Tessa Daniels." Tessa smiled

"Ok, we will be in touch. If any of you other ladies have any information let me know." Booth handed all the women one of his cards.

When Booth and Brennan reached the SUV they decided to go have lunch seeing as it was 1:30.

__________________________________B3B_________________________________

Brennan and Booth settled into their usual spot at the diner and the waitress brought them their usual orders without asking.

"I bet the guy hangs around parks waiting." Brennan took a fry from Booth's plate.

"Yeah, I will bring the nanny in and see if she remembers any one suspicious hanging around the day Hannah disappeared."

"Are you going to interrogate her after lunch?" Brennan asked

"Probably, why do you want to tag along?" Booth smiled knowingly. Brennan just smiled back in response.

They finished up their lunches and then headed to the Hoover to interrogate Isabel.

____________________________________B3B_______________________________

"Hi, Miss Davis, we just want to ask you a few questions about Hannah Richards' disappearance." Booth went into FBI mode

"Well, we were at the park and she said she was going to go down the slide. I told her ok come right back when you're done. I waited for her for about 10 minutes, but she never came back." Isabel shook her head as tears fell down her face.

"Right, now that day did you notice anyone hanging around that looked odd." Brennan asked

"ummm, there was this one guy hanging around the slide. He was just sitting there." Isabel said confused. "Wait, as soon as Hannah went over to the slide he was gone too." Isabel added as a sudden realization came over her.

"Had you ever seen him there before?" Booth asked

"Yes, all the time. No one thought anything of him though." Isabel cried harder

"Could you describe him to our forensic artist?" Booth asked

"I think so." Isabel nodded

"Ok we will bring her in. One more thing did you ever see any of these girls at the park?" Brennan fanned the photos of the 4 other girls across the table.

"Oh my gosh, yes. All of them!" Isabel was in shock. Booth and Brennan nodded. After a few more questions they sent in Angela.

Angela was able to create a face from Isabel's description. When she ran it through the database it matched Clark Reed's photo. When Angela showed the photo of Clark Reed to Isabel she said it was him.

Booth and Brennan didn't have enough evidence to bring him in so they spent the rest of the day trying to connect him to the other murders. What they didn't know was that Clark had seen them at the park and realized he was about to get caught. He had to find a way to stop them so he did some research on their background found the perfect way to stop them. He would target their family. He was able to find their address and from their he followed Mary, who took Matt and Ali to the park after Ali got out of school, once there he just had to wait. After 30 minutes he made his move.

__________________________________B3B________________________________

Brennan was in her office looking over some paperwork when her cell phone rang.

"Brennan" She answered

"Mary, slow down I can't understand you." Brennan became panicked

"What! No, did you look everywhere because she likes to run off." Brennan didn't want to believe it.

"Ok ok, Listen to me I want you to bring Matt to the lab. Make sure no one is following you. Do you understand?" Brennan ordered. She hung up the phone and then went to go tell Booth that one of their worst nightmares had come true. She wandered onto the platform in a daze. Booth saw she was in distress and walked over to her.

"Booth" Was all she could say at first

"Bones are you ok, what's wrong?" He placed a hand on her shoulder and turned her face to his where he saw tears in her eyes.

"Someone…someone…kid…kidnapped…Alison." Brennan didn't even try to hide the tears which were flowing freely. The rest of the team looked up in shock, but didn't say anything.

"What, how did this happen." Booth went into protector mode

"Mary took the kids to the park, she was watching Ali play and then she bent down to pick up a toy Matt dropped. When she looked up Ali was gone." Brennan spoke through sobs.

"Is Matt ok?" Booth tried to think clearly through the rage

"Yes, I'm having Mary bring him here." Brennan gained control of her self.

"Good. Look Bones we will get through this. You need to be strong for Ali. I know this is hard, but we have to stay strong and focused" Booth tried to hide his own tears as he pulled her into a hug and held her for a long time both of them oblivious to the other team members standing on the platform. When they pulled apart they faced the rest of the team.

"Booth, Brennan we will do whatever we can to help you find her." Cam spoke first.

"You will find her." Hodgins added.

Within minutes everyone was back to work trying to catch Clark and find Ali. Brennan paced her office waiting for Mary to bring Matt; Booth stayed with her, Cam directed the rest of the team.

When Mary arrived Brennan immediately took the car seat from Mary and took Matt out of it and held him. Booth got the full story of what happened and then let Mary go home reassuring her it was not her fault.

Brennan turned to Booth. "We have to find her Booth. She's not even 2 and a half yet." She looked into his eyes and Booth was able to see the unspoken emotion.

"I know Bones, I know." Booth maintained eye contact, his own eyes reflecting the same emotions.

**AN: Welllllllllllllll I hope you liked this chapter. I hope it isn't too confusing, if it is just ask questions and I will answer. I hope Brennan wasn't too OOC, but I figured having kids would change her. Anyway please review…….the more you review the faster I update. Any comments, questions, or concerns are welcome. **


	3. Chapter 3

**AN: Hello…….sorry for the long wait for an update. I have been busy with school and swim practice. Also I didn't get the response I wanted. If you want me to update faster you need to review and let me know what you think whether it's good or bad. Any way here is another chapter.**

It had been two days since Ali had gone missing. Booth and Brennan had tried to track down Clark Reed, but he had disappeared. His house was empty and there had been no action his credit cards. The team was at a loss what to do next.

Booth and Brennan had made Brennan's office their home for the past two days. They took turns alternating between working and watching Matt who they hadn't let out of their sights. Occasionally they would sleep but only for a few hours. Brennan refused to sleep and often worked until she passed out from exhaustion. Booth attempted to make her sleep and eat, but he too was too drained to fight her.

"Hey Bones, I brought you some coffee." Booth set the coffee on the table in front of Brennan who was again sleeping at the work table on the platform. Booth nudged her awake with his free hand as he cradled a sleeping Matt in his other arm.

"What time is it?" Brennan mumbled as she sat up

"7 AM" Booth answered with no emotion his voice

"Ok let's get to work." Brennan stood up from the chair.

"Let go put Matt down and I will be right back." Booth turned and headed back to Brennan's office while Brennan began working where she had left off.

On his way back to the platform Booth ran into Wendell

"Hey Booth." Wendell looked up from the report he was reading

"Hey, were you working with Bones last night?" Booth asked

"Yeah, why?" Wendell asked

"What time did she fall asleep?" Booth gave Wendell a look that said he had better tell the truth.

"Ummmm I left around 1 and she was still going so sometime after that. She said she was going to be working for a while though." Wendell gave Booth a sympathetic look.

"Thanks, man let me know if anything comes up in the case ok." The men parted ways and went on with their business.

When Booth reached the platform Brennan was examining a bone from the most recent victim.

"Did you find something Bones?" Booth asked as he swiped his card

"Yes, I think that there is particulate they may tell us where she was killed. If we can figure out where that is we may be able to find Ali." Brennan answered. Booth was getting ready to respond when Cam came up on the platform carrying an envelope.

"Dr. Brennan, this came for you. There is no return address" Cam handed the envelope to Brennan who sat down to open it.

Once it was opened Brennan dumped the contents of the envelope onto the table and let out a smell gasp. The envelope contained a necklace, a lock of hair and a note. All the contents had blood on them.

"Booth, that's her necklace…" Brennan finally spoke

"I know Bones, and that's her hair. What does the note say?" Booth picked up the note.

"Stay away or she dies." Booth repeated the words from the note.

"That means she's still alive right?" Brennan asked hopefully

"Yes, Dr. Brennan it does." Cam tried to give Brennan a hopeful smile. The situation was starting to worry her because both booth and Brennan had become very calm and that could only mean that they were both going to break soon.

"Maybe Hodgins can find some particulates." Brennan attempted to remain calm.

"Hey Hodgins, come here!" Booth shouted as he saw Hodgins and Angela walk through the lab ready to work.

"What's going on?" Hodgins asked somberly

"We need to analyze some particulates." Booth handed Hodgins the envelope and its contents. Brennan who remembered the particulates in the bone went over and retrieved that too.

"I will let you know what I find man." Hodgins set off to get to work.

"What do we do now?" Brennan looked to Booth

"Now Bones, we wait. That's all we can do. I'm going to go eat some breakfast, want to come?" Booth asked hopefully

"No, I'm not hungry. I think I will just work." Brennan answered without looking at Booth.

"I will join you Booth." Cam offered

Brennan turned back to the remains that were on the table. Angela who had been standing on the platform heard the whole conversation and after Booth and Cam left she approached Brennan.

"Sweetie…" Angela started

"What Ange?" Brennan interrupted rather quickly.

"Why don't you take a break?" Angela put her hand on Brennan's shoulder

"I can't. I have to keep working until I find her." Brennan turned around and faced her friend. Her eyes were full of tears, but none of them ran down her face.

"Look at your self sweetie. You have hardly slept in days." Angela looked at her friend sympathetically

"I can't sleep because when I do I have nightmares." Brennan admitted as the tears started to roll down her face. "Every time I close my eyes I picture her hurt and scared somewhere. So that's why I can't…I just…I can't." Brennan didn't finish

"Oh sweetie" Angela wrapped her friend in a hug. "We will find her. I promise." Angela whispered into her friend's hair a she cried.

Booth and Cam had gone to the cafeteria to eat. After they got their food they found a table and began to eat in silence.

"How are you holding up big man?" Cam asked

"I'm fine Cam." Booth answered curtly

"Right…" Cam rolled her eyes

"I just want to find her ok." Booth tried to end the conversation

"We all do Booth, and we will." Cam gave him a reassuring look

"Thanks Cam" Booth looked down at his plate and they continued eating in silence.

It wasn't until close to lunch that Hodgins was done analyzing the particulates. He tracked down Boot and Brennan who were in Brennan's office. Booth was taking a nap and Brennan was working at her desk with Matt on her lap. When she heard Hodgins tap on the door frame she looked up.

"Hey, did finish with the particulates?" Brennan asked

"Yeah, is now a good time?" Hodgins motioned towards Booth.

"I'm awake Hodgins." Booth said

"Ok, well I was able to trace the dirt to an area in the mountains of North Carolina. It is specific to this area right here." Hodgins showed Brennan the map.

"Wow, that's a small area. Once we get there we should be able to pin point where his killing area is." Brennan said.

Booth sat up and rubbed his eyes. "I will call the FBI and get a tact team together. We need to be careful thought because we don't want to spook this guy again.

Within an hour everything was arranged. The whole team insisted on coming. By 3 they had made it to North Carolina.

The FBI was able to find out that Clark Reed rented an old storage unit on the outskirts of town. Booth and Brennan and the rest of the tact team headed there. Cam, Hodgins and Angela stayed behind in the main town with Matt.

"Ok listen, we surround the building, and go in quickly and quietly." Booth said "Bones stay close." The team surrounded the building and waited for Booth's count.

Booth counted to three and then they went into action. "FBI freeze!" He shouted as they opened the storage unit.

Clark was sitting in the middle of the unit with a remote in his hand. "I have been waiting for you Agent Booth." Reed said calmly

"Where is Ali?" Booth remained focused

"Not here." Reed replied. "Would you like to here her voice?" Reed pressed a button on the remote he was holding and suddenly the room was filled with Ali's screams and pleas to stop. Suddenly the tape was silent.

"Where is she?" Brennan demanded

"I buried her." Reed coolly answered

"You son of a bitch!" Booth charged Reed and placed his gun to his head. "Where is she! Tell me now or I swear to God I will blow your brains out!" Booth shouted

"Booth stop." Brennan came up to Booth and placed her hand on Booth's arm.

Booth calmed down enough to place the handcuffs on Reed and take him into custody. After the team left Booth and Brennan were left alone. "She could still be alive." Brennan said as she pulled out her phone to call Angela.

After 10 minutes Hodgins, Cam, and Angela arrived with Matt. The ream went over the storage unit until Hodgins found something.

"Look a this, this dirt isn't from around here."

"Where is it found Hodgins?"

"About 10 miles south of here. I can pin point the location with my computer" Hodgins answered

"Booth, we got to go." Brennan said. Everyone was back in their cars and Booth called the FBI team back in while Hodgins directed Booth where to drive.

When they reached the area where the dirt could be found they began to search. A few minutes later the FBI team had arrived again.

"Look for any recently dug up dirt." Brennan directed

"Over here!" An FBI agent called

Brennan and Booth ran over to where the agent was and began to dig. After a minute of digging they uncovered Ali's arm. Hodgins and Cam came over help. "We got her!" Booth shouted as Brennan uncovered the rest of Ali." Her tiny body was beaten, bloody and unconscious.

Brennan and Cam pulled Ali out of the dirt and laid her down to examine her.

"She's not waking up! Why isn't she waking up?" Brennan panicked as she checked her breathing. "She isn't breathing!" Brennan began CPR.

"Come on Ali!" Brennan shouted between breaths and tears. "Come on!" No one said a thing as they waited for the little girl to breathe.

Suddenly Ali's chest moved and she coughed. Brennan sat back on her heals and breathed a sigh of relief as Booth came over.

"It's all over baby girl, daddy's got you." Booth scooped up his daughter who was still unconscious in his arms and put her in the ambulance that was waiting.

Brennan stayed where she was on the ground too shocked to move. After the ambulance left Booth came over and helped her up.

"It's over Bones, you can breathe now." Booth looked at Brennan who had tears running down her face and wiped them away as he wrapped her in a hug. Then Hodgins, Cam, and Angela came over and brought Matt.

"Hey there big man!" Booth said through his own tears as he took Matt in his arms. Angela gave Brennan a hug. Hodgins and Cam were busy playing with Matt who was in Booth's arms.

"I think we should head to the hospital." Brennan finally said.

"Oh yeah." Booth and the rest of the team headed to their cars and drove to the hospital.

"When will they let us see her?" Brennan asked impatiently.

"Soon Bones, soon." Booth sighed

The rest of the team had gone home knowing Booth and Brennan would need some time to them selves. Hodgins and Angela had also offered to take Matt for the night.

It was another hour before the doctor came out to talk to them. "Mr. and Mrs. Booth?" the doctor approached

"Yes." Booth and Brennan stood up

"Alison is doing very well. She has a broken wrist, 2 broken ribs, a concussion, and several cuts and bruises. We were able to repair the internal bleeding from the broken ribs with surgery."

"So she's going to be ok?" Booth asked

"Yes we believe so. We did find ketamine in her system and we won't know what the effects of that will be until she wakes up." The doctor added

"Was she….you know touched?" Booth asked awkwardly

"No, there were no signs of rape. I can take you to her room now if you want. We did have to intubate her so she will have a tube in her throat just so you know." The doctor answered.

Booth and Brennan followed the doctor down the hall to Ali's room. When they got there they took in the sight of their little girl. She was hooked up to all sorts of monitors. Her face was covered in cuts and bruises and there was tube coming out of her mouth. Brennan grabbed Booth's hand as they entered the room.

They sat in chairs in silence until they both drifted off to sleep. In the morning Booth was the first to wake up and noticed that sometime in the night Brennan had moved to the bed with Ali. He smiled at the sight of both his girls sleeping soundly. After staring for a moment longer Booth went to get some coffee.

When Booth came back Brennan was awake, but still in the bed. She was stroking Ali's hair and when Booth came in she looked up at him.

"Hey." Brennan whispered

"Hey" Booth went over and gave both Brennan and Ali a kiss. "I brought you some coffee."

"Thanks." Brennan got out of the bed and took the cup Booth held out to her.

The doctor came in and checked on Ali a little while later and told them she would most likely be awake soon.

Angela called and let Brennan know she and Hodgins were on their way and Cam would be down later. By the time Hodgins and Angela arrived Ali started to stir.

She blinked her eyes once or twice and started to move her hand to the tube in her throat. Brennan who had been holding Matt handed Matt to Angela and went over to her daughter's bed. Booth followed close behind.

"Hey there baby girl." Brennan brushed Ali's hair away from her face and placed a kiss on her forehead.

"Everything's going to be fine. Mommy and daddy are here now." Booth took his daughter's tiny hands in his own big hands and kissed them.

Hodgins had gone to notify the doctors that Ali was awake and they came in immediately. The doctors forced Booth and Brennan out of the way. They removed the tube after making sure Ali could breathe on her own. After making sure she was stable the doctors left and said they would be back later.

"There you go honey all better." Brennan returned to her daughter's side and took her hand.

"Where am I?" Ali asked still in a daze

"You're in a hospital because a bad man hurt you." Brennan answered

"You're safe now though ok princess." Booth reassured her.

"Can I see Matty?" Ali asked finally noticing Angela holding Matt standing by the door with Hodgins. Angela smiled and brought Matt to his big sister.

"Hi little brother!" Ali leaned over and gave Matt a kiss.

"He missed you sweetie. We all did." Angela gave Ali a kiss.

"I was scared Auntie Angie." Ali began to cry as the memories came back to her.

Booth got into bed with Ali and sat her in his lap as he wrapped his arms around her small body. "Shhhhhhhhh don't cry baby its over." Booth whispered in her ear.

Ali finally stopped crying and lifted her head up when she heard another familiar voice. "Cam!" Ali smiled at the pathologist.

"Hey there Ali." Cam smiled at Ali "How are you feeling?"

"I'm ok." Ali smiled her Booth charm smile

A silence fell over the group which Cam quickly ended. "Ok, well why me Angela and Hodgins don't see what they have in the cafeteria to eat." Cam gave Angela and Hodgins a knowing glance."

"Ok , yes, right." Hodgins caught on and Angela handed Matt over to Brennan who was sitting in a chair next to Ali's bed.

"We will be back in an hour or so." Angela smiled and the three left the room

After everyone left Brennan and Matt joined Ali and Booth in the hospital bed. Ali settled in between her parents and Brennan settled Matt on her lap.

"My stomach hurts daddy." Ali whined as the pain medicine began to wear off.

"I know sweetie. Do you want me to ask the nurse for some more medicine?" Booth looked down at his daughter with concern.

"uhuh." Ali buried her head into Brennan's shoulder as she began to cry. Brennan wrapped her free arm around Ali and looked at Booth.

"Ok, don't cry princess. I'll go get the nurse." Booth got out of bed and left the room in search of a nurse. He quickly returned with a young nurse behind him. Brennan got out of bed to let the nurse do her job.

"Hi Ali, my name is Sarah." The nurse smiled

"Hi Sarah." Ali answered through tears

"How much does your stomach hurt?" Sarah asked

"A lot." Ali cried harder.

"Look can you just giver her some pain medicine already." Brennan interrupted as see bounced Matt on hip.

"Yes of course." Sarah answered taken aback. She left the room to get the medicine and returned quickly with a syringe. She injected the medicine in to Ali's IV. "There you go Ali. You should start feeling better now" Sarah smiled and left the room.

As the drugs started to take affect Ali became sleepy. Brennan helped her lay back in the bed and then kissed her forehead as she drifted off.

"She should sleep for a while." Brennan said

"Yeah." Booth added

"Do you want to go get something to eat? She won't notice." Booth asked

Brennan nodded and followed Booth out the door. They met up with Cam, Hodgins and Angela in the cafeteria. After eating Cam, Hodgins, and Angela headed back to D.C while Booth and Brennan went back to Ali's room.

After spending a week in the hospital Ali was able to go home. Most of her bruises were gone and she was starting to act like her normal self.

When they arrived home Ali unbuckled her car seat and ran to front door. "I'm home!" Ali laughed

"Ali stop running. You're going to fall." Brennan shouted as she pulled Matt's car seat out of the car.

Booth chased after Ali and scooped her up as he unlocked the front door. Brennan followed in behind with Matt.

"Are you glad to be home Ali?" Brennan asked as she set Matt's car seat down on the kitchen and began to unbuckle him.

"Yeah!" Ali ran into the living room and started playing with her toys. Booth followed after her and Brennan listened as they talked and Ali explained the game they were playing.

"Gah!" Matt interrupted Brennan's thoughts

"That's right my big man. You are 5 months old today!" Brennan picked up Matt and began blowing raspberries on his stomach. Matt squealed with delight.

"Hey Bones, you two gonna come join us?" Booth walked into the kitchen wearing a pink tiara and a wand.

"Yeah, we're coming Booth." Brennan laughed

**AN: ok well I hope you enjoyed this chapter. Sorry it took so long for me to update. Life just got really crazy and I lost my inspiration. Let me know if you have any ideas where you would like to see this story go. Please comment**


	4. Chapter 4

**Ok here's another chapter. This chapter is kind of a filler chapter to help move this story along. There will be a bit more angst coming up, but first some fluff. **

It was a Saturday afternoon and Brennan was on her way to Angela's house for lunch. It had been 2 months since Ali's kidnapping and she was finally completely healed and ready to play.

"Mommy are we there yet?" Ali asked impatiently from the backseat.

"Yes, sweetie we will be there soon." Brennan looked at her daughter in the rearview mirror and smiled.

"I miss Savannah." Ali sighed as she stared out the window.

"I know, that's why we are going over to play today." Brennan responded.

After another 5 minutes of driving Brennan pulled up to the Hodgins' mansion. She parked her car and went around to the back of the car to get Matt and his car seat while Ali quickly unbuckled her self and hopped out of the car.

"Ali ring the doorbell first." Brennan shouted as Ali started to open the door.

By the time Brennan got to the door with Matt Angela had already answered the door and was greeting Ali who was jumping around excitedly.

"Where is Savannah?" Ali asked

"Ali!" Savannah shouted from the top of the stairs and came running down to give her friend a hug. "I got a new doll house. I'll show you." Savannah took Ali's hand and pulled her towards the playroom.

Angela and Brennan laughed at their daughters and went to the kitchen where Brennan helped Angela finish making lunch.

"How is everything going at your house Bren?" Angela asked as she mixed together a salad

"Good. Ali loves school and Matt is starting crawl like crazy and he gets into everything. Isn't that right big guy?" Brennan turned and smiled at Matt who was sitting in his car seat.

"He is getting really big. He looks a lot like Booth except for the hair and eyes of course." Angela smiled. "Speaking of Booth how is the G man?"

"Booth is. Well he's just being Booth." Brennan answered cryptically

"And what does that mean?" Angela asked

"He is just being really protective. He got a state of the art alarm system installed last week and he is always watching over Ali."

"Well he's just concerned." Angela pulled down four plates and began to put salad on each one

"I know, but I want Ali to feel safe and Booth watching her like she might disappear at any minute isn't helping." Brennan added sandwiches to the plates and set them around the table. "Ali still has nightmares. It takes 30 minutes to get her to go to sleep, and Booth won't even look at his son half the time." Brennan paused and tried to keep her emotions in check.

"It's ok, sweetie Booth will come around. He's just coping in his own way. Booth is just afraid of losing what he has and he probably feels guilty for loving Matt while Ali was missing." Angela placed a hand on her friends shoulder. "Let's just have a nice day and not worry about everything ok. I'll go get the girls." Angela left the kitchen and went to find Ali and Savannah.

The rest of the day was uneventful; the girls played dress up while Brennan and Angela watched over Matt and talked about names for the twins. At 3 Brennan packed up Matt and Ali and headed home.

_BB_

When Brennan arrived home she sent Ali to the playroom and put Matt in his crib since he had fallen asleep. Brennan then spent the rest of the day playing with Ali while she waited for Booth to come home from his weekend with Parker. At 5 Booth came home.

Ali eagerly greeted her father when she heard him come in. "Daddy your home!"

"Yes I am. How's my princess?" Booth picked her up and wandered into the kitchen where Brennan and Matt were working on dinner.

"Hey!" Brennan smiled when she saw her husband.

"Hey" Booth smiled back as he let Ali down. Booth went over to Brennan and wrapped his arms around her as he kissed her. "I missed you" Booth smiled

"I missed you too and so did Matt. Where's Parker, I thought we were keeping him for the week?" Brennan went back to cooking dinner.

"Rebecca decided that since Parker has so many things going on this week he should stay with her. She did say we could have him next week though." Booth offered a small smile even though he was a little hurt.

"Well at least we get him next week. Anyway, are you going to say hi to your other son who is right here asking for you?" Brennan snapped

"Of course I was, Bones what has been going on with you lately?" Booth snapped back as he went over to Matt.

"What's going on with me? What's going on with you?" Brennan snapped again. "You go around acting like Ali is glass and she could break at any moment. Ali is still freaked out because you are scaring her with the way you act. You have alarms installed, you watch over her every waking moment yet can't find the time to even hold your son when all he wants is his father! So don't tell me there is something wrong with way I'm acting!" Brennan paused when Matt started crying and Booth didn't make a move to pick him up. "You know what just forget it. I will take care of him!" Brennan picked up Matt and left the kitchen.

Booth was stunned; he and Bones had never had a fight like this. All he could do was go after her. "Bones, wait I'm sorry. Can we talk about this?" Booth was pleading.

"Oh, you want to talk now? Well I don't." Brennan set Matt down on the changing table and changed his diaper.

"Bones, stop yelling. Ali is going to here us and then we are going to have to explain why mommy and daddy are yelling. Matt is already upset by the noise too." Booth tried to remain calm.

"Fine then this discussion is over. Dinner will be ready in thirty minutes." Brennan picked Matt back up and went to finish dinner. Booth sighed and slammed his palm against the changing table. He calmed himself down and went to go play with Ali.

Dinner was eaten in icy silence. The only conversation came from Ali who told he father all about her day with Savannah. After dinner Booth spent the evening in the playroom with Ali while Brennan sat on the couch with Matt and worked on her latest book.

At 7:30 Booth took Matt and Ali to get baths and then put them to bed. After they were asleep Booth went into his and Brennan's bedroom where Brennan was already in bed reading an anthropology journal. Booth slipped into bed beside her and attempted to make conversation.

"Bones, I'm sorry. Your right, I was acting crazy and I was ignoring Matt." Booth waited for a response but didn't get one. He sighed and picked up the book he had been reading.

"I just don't understand, I want to, but I don't." Brennan put her journal down and looked at Booth.

"It's complicated Bones. I love our children I really do. But when Ali was missing I felt so guilty that Matt was here with us and I could take care of him and protect him when I couldn't do that for Ali. When we found her I felt like I had to make it up to her. I guess I messed up huh?" Booth chanced a look at Brennan who was laughing. "Bones, this isn't funny I'm trying to tell you I messed up and your laughing?"

"I'm sorry it's just you really did mess up, but so did I. I never tried to get you to talk I just waited until I exploded. We are one messed pair aren't we?" Brennan laughed again and this time Booth joined her. "Yeah we really are a pair. But, were good now right?" Booth asked. "Yeah we're good." Brennan and Booth kissed.

_BB_

Sunday was spent relaxing around the house after a pancake breakfast made by Booth. Ali wanted to go to the park so they packed up and went to the park. Booth took Matt and Ali to swings and watched as both kids squealed in delight. After playing for a while they settled on a blanket and ate the lunch Brennan packed.

When they got home both kids were exhausted and took naps. Booth and Brennan took advantage of the peace and quiet to talk about a recent case they were working on. At 2 Matt woke up. Booth went to go pick him up.

"Hey little big man, how was your nap?" Booth picked up Matt and checked his diaper which was dirty. He took Matt over to the changing table to change his diaper when he noticed that Matt was a little warm. "Whoa little man your burning up, lets see if you have a fever." Booth carried a still crying Matt downstairs to where Brennan was. "Hey Bones, where's the thermometer, I think Matt has a fever."

"It's in the medicine cabinet in Ali's bathroom." Brennan got up from the couch and followed Booth upstairs.

"It's ok baby, shhhh shhh" Brennan tried to soothe Matt as Booth stuck the thermometer in Matt's ear. When thermometer beeped Booth took it out and read the temperature. "There it is 99.7 he's got a fever."

"Poor guy, you must feel awful." Brennan picked up Matt who finally stopped crying. Suddenly Ali appeared in the doorway of Matt's room.

"Hey its sleeping beauty, she has awoken from her slumber." Booth smiled at Ali

"I'm not a princess daddy. Why does Matty feel awful?" Ali looked at her mother with sad blue eyes.

"Matt just has little fever that's all. Why don't you take daddy downstairs and play a game." Brennan reassured her daughter. Booth took Ali's hand and led her downstairs. Brennan spent a few more minutes trying to get to calm down since he had started to cry again. Once he was clam she went downstairs and joined Booth and Ali.

Booth and Brennan spent the rest of the day between entertaining Ali and taking care of Matt who seemed to be getting worse.

Booth was changing Matt's diaper when Matt threw-up. "Ok buddy, that's not good. Maybe we should take you to a doctor. Let's see what mommy thinks." Booth called Bones upstairs.

"Booth, what's wrong? Can't you change a diaper on your own?" Brennan joked, but when she saw Matt the smile was wiped off her face. "He's throwing up now? This is probably more than a regular virus." Brennan took over changing his diaper. "Hey, Booth how long has he had this rash?" Brennan noticed a rash on Matt's stomach.

"I don't know, I didn't even notice it." Booth saw the concern in Brennan's eyes. "Why? What does it mean?"

"Vomiting, fever, irritability, not eating…it couldn't be." Brennan went into squint mode

"Bones, what is it? How bad is it?" Booth looked at his son who was still crying.

"It could be meningitis." Brennan said

"You mean the kissing disease, he's just a baby." Booth stated

"I know but he could have just picked it up." Brennan said. "Booth, if it is meningitis its serious and we are all at risk. We need to go the hospital now!" Brennan looked at Booth with fear in her eyes.

Booth sighed and looked a Brennan"Ok, let's go.".


End file.
